369 add ID signatures in sigprofilerassignment#429
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efigb
commented
Mar 13, 2026
efigb
commented
Mar 13, 2026
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I commented this since I'm not sure it's correct
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Pull request overview
Adds indel (COSMIC ID) signature fitting to the deepCSA workflow by extracting the ID83 matrix from SigProfilerMatrixGenerator outputs and running SigProfilerAssignment cosmic_fit with context_type=ID.
Changes:
- Add an indel reference signatures parameter (
indel_ref_signatures) and load it into the main workflow. - Extend SigProfilerAssignment
cosmic_fitmodule to accept a configurablecontext_typeand incorporate it into output naming. - Wire ID83 matrix output into a new SigProfilerAssignment invocation configured via
conf/modules.config.
Reviewed changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| workflows/deepcsa.nf | Adds ID83 matrix extraction + indel signature assignment step in the signatures branch. |
| nextflow.config | Introduces default path for indel_ref_signatures. |
| modules/local/signatures/sigprofiler/matrixgenerator/main.nf | Exposes an matrix_ID83 emitted output for downstream consumption. |
| modules/local/signatures/sigprofiler/assignment/cosmic_fit/main.nf | Adds context_type support and includes it in output naming + CLI args. |
| conf/modules.config | Adds SIGPROFILERASSIGNMENTINDELS config (context type + publishDir). |
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| cosmic_ref_signatures = "COSMIC_v3.4_SBS_GRCh38.txt" | ||
| indel_ref_signatures = "COSMIC_v3.4_ID_GRCh37.txt" // note that for IDs it has been defined in the GRCh37 genome version |
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@copilot apply changes based on this feedback
* Initial plan * Add indel_ref_signatures to nextflow_schema.json reference_datasets section Co-authored-by: efigb <154223352+efigb@users.noreply.github.com> --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: efigb <154223352+efigb@users.noreply.github.com>
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this branch was merged without it working well, the following commit in dev solves the issues and is fully functional |
FerriolCalvet
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adds ID signature assignment in sigprofilerassignment